[DrVenture]

Yes, you need to pull any codes and follow the data. If the main issue now is the transmission shifting improperly, then I would assume hat the transmission control module or harness/connectors got wet. A missing belly pan may have allowed more water than usual to soak those items. They should be waterproof, but on a 20 year old car may have been compromised somewhat, to begin with.

The error codes should provide a starting point.